now storing the dof-to-vertex mapping in the model object when serial…

…ized

pyurdme/pyurdme.py

@@ -150,6 +150,7 @@ def __setstate__(self, state):
                     mesh.constrained_domain = compiled_object
                 if 'num_dof_voxels' in state['mesh']:
                     mesh.num_dof_voxels = state['mesh']['num_dof_voxels']
+                mesh.init(2, 0)
                 self.__dict__['mesh'] = mesh
             except Exception as e:
                 print "Error unpickling model, could not recreate the mesh."
@@ -1239,6 +1240,10 @@ def __getstate__(self):
 
         state = self.__dict__
         state["filecontents"] = filecontents
+        state["v2d"] = self.get_v2d()
+        state["d2v"] = self.get_d2v()
+
+
         for key, item in state.items():
             try:
                 pickle.dumps(item)
@@ -1265,11 +1270,26 @@ def __setstate__(self, state):
         for k,v in state.items():
             self.__dict__[k] = v
 
+    def get_v2d(self):
+        """ Return the vertex-to-dof mapping. """
+        if not hasattr(self, 'v2d'):
+            fs = self.model.mesh.get_function_space()
+            self.v2d = dolfin.vertex_to_dof_map(fs)
+
+        return self.v2d
+
+    def get_d2v(self):
+        """ Return the dof-to-vertex mapping. """
+        if not hasattr(self, 'd2v'):
+            fs = self.model.mesh.get_function_space()
+            self.d2v = dolfin.dof_to_vertex_map(fs)
+
+        return self.d2v
+
     def _reorder_dof_to_voxel(self, M, num_species=None):
         """ Reorder the colums of M from dof ordering to vertex ordering. """
 
-        fs = self.model.mesh.get_function_space()
-        v2d = dolfin.vertex_to_dof_map(fs)
+        v2d = self.get_v2d()
         if len(M.shape) == 1:
             num_timepoints = 1
         else:
@@ -1424,8 +1444,8 @@ def _initialize_sol(self):
             raise URDMEError("URDMEResult.model must be set before the sol attribute can be accessed.")
         numvox = self.model.mesh.num_vertices()
         fs = self.model.mesh.get_function_space()
-        vertex_to_dof_map = dolfin.vertex_to_dof_map(fs)
-        dof_to_vertex_map = dolfin.dof_to_vertex_map(fs)
+        vertex_to_dof_map = self.get_v2d()
+        dof_to_vertex_map = self.get_d2v()
 
         # The result is loaded in dolfin Functions, one for each species and time point
         for i, spec in enumerate(self.model.listOfSpecies):
@@ -1607,8 +1627,7 @@ def _copynumber_to_concentration(self,copy_number_data):
             where the volume unit is defined by the user input.
         """
 
-        fs = self.model.mesh.get_function_space()
-        v2d = dolfin.vertex_to_dof_map(fs)
+        v2d = self.get_v2d()
         shape = numpy.shape(copy_number_data)
         if len(shape) == 1:
             shape = (1,shape[0])